annot_from_db: Annotate from Database

In octopode/tidychrom: A Dead Simple Toolkit for Quantitative Chromatography

Annotate from Database

Description

Simple iterative database search to annotate spectra in a tibble

Usage

annot_from_db(spectra, dir_db, bin, fname_regex = "*.mzXML", cores = 1)

Arguments

spectra	Grouped (e.g. by scan tibble with columns mz, intensity.
dir_db	Directory containing database spectrum files in an mzR-readable format (mzXML, mzML, etc.)
fname_regex	Regex string that can be used to prefilter database files (generally the suffix.)

Value

A summary of the input tibble with additional columns: file (basename of the best-matching database spectrum file) cos (cosine matchup score for that file)

Examples

# effectively add an annotation column to peaks_matched:
peaks_matched <- annot_from_db(peaks_matched, "~/msdb/", "methyl")

octopode/tidychrom documentation built on Nov. 2, 2022, 1:32 a.m.